Monday, July 5, 2010

Genomic Junk and Evolution

Evolution was claimed to be an undeniable fact in the nineteenth century so today new proofs hardly seem necessary. But science continues to offer them up, say evolutionists, as we probe the depths of biology. These days a common source of such proofs is the genomic data which exploded onto the scene in recent decades. But are the new data really undeniable confirmations of Enlightenment speculation or are the new data merely interpreted according to the same old metaphysics?

The genomic revolution has taught us that genomes contain far more than an inventory of genes. Included is a genomic cast of characters, including viruses, pseudogenes, and LINEs and SINEs (long and short interspersed elements, respectively), to name a few. Evolutionists were quick to find that such intruders were not only useless junk but in accordance with common descent—they appear in the same genetic location in cousin species. Such evidence, according to evolutionists, proved their theory yet again, and once and for all.

The molecular revolution was providing the usual evidence of dysteleology, but it was coupled with commonality across species. The so-called shared error evidence, like identical typos in homework assignments from different students, provided the ultimate proof text of a common source. There could no longer be any doubt, evolution was mandated by the evidence.

Evidential Problems

Indeed there is much evidence here that supports evolution. But there are problems as well. Occasionally, for instance, this genomic junk does not align with the pattern required by common descent but instead mysteriously appears where it shouldn’t (such as in distant species rather than close cousins) or is absent from where it should be (such as in a particular species among many).

Such anomalies can be explained by various mechanisms. Perhaps junk occasionally goes missing because it failed to become fixed in the population, though it succeeded in cousin species. Or perhaps DNA repair processes sometimes erase the junk repeatedly and independently in cousin species. Or perhaps insertion site preferences cause the same pattern to appear in distant species.

Aside from speculation, we don’t know how evolution created such mechanisms. But given their existence and utility in explaining anomalous patterns, this means that evolutionists can explain a wide variety of patterns. And that means the particular pattern we do observe is less compelling evidence for evolution.

The Finding of Function and Theory-Dependent Interpretations of Evidence

Another problem altogether is the failure of the evolutionary expectation (and triumphant proclamation) that these genomic intruders are nothing more than junk. In fact this so-called junk has occasionally been discovered to perform various functions, such as in embryonic development and gene regulation. Indeed evolutionists have had to conclude that this junk actually played an important role in, yes, evolution itself.

But if you already believe that all of biology just happened to arise by itself, then it is hardly a challenge to believe that retro viruses and the like could have serendipitously played important roles in the narrative. Philosophers refer to this as theory-dependent observations. The evolutionist’s credulous interpretation is a consequence of the fact that they are evolutionists to begin with.

From a theory-neutral perspective these functions cast a long shadow on evolution. Are we simply and automatically to believe that evolution just happened to create retro viruses which then, in turn, just happened to play crucial roles in the evolution of the species?

The Religion in Evolution

Given these conundrums one might think evolutionists would go easy on these evidences. There certainly is plenty of supporting evidence, but there are complicating questions. The complicating questions, however, have to do with the details of evolutionary history. How could this happen and how could that happen?

Those are merely the details of evolutionary theory, and evolutionary theory never was motivated by the liklihood of evolution. Evolutionary theory is, and always has been, motivated by the mandate for naturalistic explanation. As so many Christians have argued, naturalism is required for both philosophy and theology. Both man and god need a natural history, for anything less is bad science and bad religion.

In this case, it is obvious that god never would have designed or created pseudogenes, viruses and the rest of the genomic malcontents. We would have to believe, as Ken Miller explains, that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. As Elliot Sober has pointed out, this is the Darwinian principle—it is not that the probability of the evidence is so high on evolution, but that it is so low on creation.

Whether the pattern always fits, or whether unlikely functions are discovered, is altogether irrelevant. Yes, they reduce the probability of the evidence on evolution, but so what? What’s the difference between 0.1/0 and 0.01/0? Either way evolution wins.

This is evolutionary thinking. Darwin and evolutionists before and after, evaluate the evidence on creation and find it wanting. Furthermore naturalistic explanation is necessary for good science. Evolutionary theory is unlikely, but necessarily true, for the alternatives are both false and not allowed anyway.

Yes there is evidence for evolution in the genome. It is complicated but any objective analysis would tally points for Darwin. But those points would have to be compared to the many other evidences, both for and against the theory. The problematic evidences are formidable and evolution would not emerge unscathed. The genomic evidence in particular, and the totality of evidence in general, do not bode well for evolution, whichever version one favors. The idea from Kent certainly would not qualify for anything close to the status of fact. Unless, that is, the idea had to be true. Religion drives science and it matters.

There's quite a lot in your latest post. To take the simplest matter first, I am not convinced that evolutionists expected that genomic "junk" would have no function. I have read that Ernst Mayr, at least, assumed that natural selection would quickly weed out nonfunctional elements in the genome. Dawkins famously extended his gene-centric approach to this question, suggesting that many of these sequences were essentially parasitic, remaining in the genome because they were good at surviving, not because they helped us to.

Certainly it would be odd to suppose that such "junk" could not perform useful roles: an endogenous retrovirus or pseudogene would be like any other mutation, likely neutral, possibly harmful, but on rare occasions beneficial (and hence more likely to stick around than harmful ones). It is true that a number of pseudogenes and ERVs are known to perform some sort of function, but most are not. It is also known from experiment that large swaths of the genome can be deleted from some species without obvious effect (though other seemingly "junk" parts cannot).

Can you cite instances in which particular pseudogenes or ERVs were found at the same loci in species thought to be only distantly related, while not being shared by more closely related species? This is the only thing you say that is actually contrary to evolutionists' expectations.

I don't think you've quite grasped the argument against teleology posed with regard to "junk" DNA. It's not that God definitely would not have done things that way (by definition, a Designer Whose motives and design philosophy are beyond our comprehension is unpredictable), but that design offers no explanation for why, e.g. pseudogenes so precisely resemble functional genes whose functions they do not share (regardless of whatever other functions they might or might not have). Likewise, it does not explain why endogenous retroviral segments bear such a detailed resemblance to actual viral genes, even though they don't function as viral genes. The Designer could not have been motivated by "common design for common function," as they don't share the functions of the things they share "design" with. It's conceivable that these just happen to be the optimal designs for whatever ineffable function He intended them to serve, but there's no obvious reason to suspect this.

In contrast, evolutionary theory offers a simple, straightforward explanation of these features: pseudogenes are "broken" copies of the formerly functional genes they resemble; ERVs are inherited remnants of actual viruses that inserted themselves into ancestral sperm or eggs. Now, you could phrase this "as the evidence is low on creation," but it would be better, I think, simply to note that creation doesn't explain it (and a Creator concerned with His creations figuring out that they were specially created might take some pains to avoid patterns of evidence that would be expected from common design), and evolution does.

You are using the old rhetorical trick. You are talking about empirical evidence and about a mandated naturalistic explanation. But what really is mandated is an empirical testable explanation no matter how you call it.

Presumably you're being sarcastic here, Dr Hunter, but naturalistic explanations are widely accepted as essential in all of science, even by committed theists. Why should evolutionary science be an exception?

Indeed, even you, in your post above, treat evolution as science, but you find "problems" with its ability to deal with all of the findings in biology. That's not a very cogent position; it sacrifices too much to your opponents and leaves you holding a rather thin bag. Maybe a better argument would be to show that evolution has nothing in common with all other sciences.

So our cells somehow knew how to take broken viruses and bad copies of genes and find uses for them? How lucky is that?

Not very, judging from the number of ERVs that have no identifiable or suspected function. You might as well wonder (perhaps you do) how a bacterium knows how to take a mutation and use it to resist penicillin, or digest nylon, or metabolize citrate. "Knowing" is not an issue; if random changes to the genome keep happening in different individuals, sooner or later one will turn up that does something useful. A great many more will turn up that cripple or kill the organism, but that is not relevant to evolution: most individuals in most species don't live to reproduce anyway, and having a harmful mutation (or harmful retroviral insertion) just moves you into the "die before you reproduce" contingent, with no particular effect on the rest of the population.

====There's quite a lot in your latest post. To take the simplest matter first, I am not convinced that evolutionists expected that genomic "junk" would have no function. I have read that Ernst Mayr, at least, assumed that natural selection would quickly weed out nonfunctional elements in the genome. Dawkins famously extended his gene-centric approach to this question, suggesting that many of these sequences were essentially parasitic, remaining in the genome because they were good at surviving, not because they helped us to.====

However one wants to characterize evolutionary expectations of the genomic "junk," the fact is evolutionists now must say it plays important biological roles, and even important roles in evolutionary history. This is a profound claim of serendipity.

====Certainly it would be odd to suppose that such "junk" could not perform useful roles: ====

Yes, but lacking the fact that such is now required by evolutionary theory, it would also be odd to suppose that such "junk" would play such important roles. Viruses happen blindly to evolve, and then they happen to play crucial roles in evolution?

====Can you cite instances in which particular pseudogenes or ERVs were found at the same loci in species thought to be only distantly related, while not being shared by more closely related species?====

You can read about HERV-K(C4), which was found in old world monkeys and humans, but not gorillas or chimps, here:

CH: You can read about HERV-K(C4), which was found in old world monkeys and humans, but not gorillas or chimps, here:

You don't even bother trying to read or understand scientific papers anymore, do you CH? AFAICT you've never read or understood a single thing about evolutionary biology.

From the paper:

The HERV-K(C4) LTR sequences (Fig. 2 C) give the predicted topology; however, as noted previously (15, 16), the provirus was missing altogether from gorilla and chimpanzee DNA, in which only an unoccupied integration site was detectable. HERV-K(C4) is found in some ape and OWM species, proving that integration occurred in a common ancestor of apes and OWMs (15, 16). The provirus is located within the human C4B gene, which arose by duplication before the separation of the apes and OWMs. The absence of HERV-K(C4) from some species is most likely caused by frequent homogenization of the C4-CYP21 locus (35), resulting in conversion back to the unoccupied integration site. Both alleles of the C4 locus (with and without the HERV-K(C4) provirus) have been identified within more than one species, suggesting that such conversions have occurred multiple times during primate evolution (35)

When will you be giving us the definition of religion for the nonstandard way you keep using the word?

====I don't think you've quite grasped the argument against teleology posed with regard to "junk" DNA. It's not that God definitely would not have done things that way (by definition, a Designer Whose motives and design philosophy are beyond our comprehension is unpredictable), but that design offers no explanation for why, e.g. pseudogenes so precisely resemble functional genes whose functions they do not share (regardless of whatever other functions they might or might not have). ====

No, I understand that. There are multiple arguments (about a dozen actually) against creation and design as I illustrated here:

http://www.darwinspredictions.com/Figure15.jpg

The "failure to provide an explanation" complaint goes back centuries and falls under the intellectual necessity in my illustration.

====Likewise, it does not explain why endogenous retroviral segments bear such a detailed resemblance to actual viral genes, even though they don't function as viral genes. The Designer could not have been motivated by "common design for common function," as they don't share the functions of the things they share "design" with. It's conceivable that these just happen to be the optimal designs for whatever ineffable function He intended them to serve, but there's no obvious reason to suspect this.====

This is a good example of the subtle metaphysics that drives evolutionary thought.

But mammals use ERV's to control the development of the placenta. I have to imagine that this is a very complex process. How did this come about through an accident?

I'm pretty sure that most of the genes involved in building the placenta are not of viral origin. What we need to account for is the incorporation of one particular viral sequence into an already-existing system, and providing something for other genes and mutations to build on.

This is a good example of the subtle metaphysics that drives evolutionary thought.

I think you mean "the subtle metaphysics of 'thought' in general.

I'm not going to ask you what you mean when you refer to evolution as "religious;" I've already encountered the creationist tendency to characterize as "religious" any idea that contradicts their particular dogmas. If you're a geocentrist, heliocentric astronomy is a religous idea based on metaphysical assumptions that are not required by "true" science. If you insist that diseases are caused by demons, then the same is true of germ theory. I assume you're neither of those, so you are content to label merely common descent and natural selection as "religious" ideas.

But the theory consistently generates false predictions.

I've looked over your "Darwin's Predictions" site. As far as I can see, for example, evolutionary theory doesn't have much at all to say about how life originated, nor does it depend on any particular account of abiogenesis, so how can it make predictions that have been falsified? Likewise, whether the genetic code is a "frozen accident" or whether there is some necessary chemical correspondence between particular codons and particular amino acids has nothing very obvious to do with common descent, natural selection, and genetic drift, or mutations to the code once it exists.

A theory does not generate false predictions simply by virtue of the fact that a person who holds a different theory on a different subject at the same time and makes false predictions based on it.

And surely there is a difference between "some mutations are more likely than others" and "mutations are random with respect to need?" If you throw a pair of dice, you're more likely to roll "seven" than "two," but which you roll is still independent of which you happen to need at the moment.

"Evolution was claimed to be an undeniable fact in the nineteenth century so today new proofs hardly seem necessary. But science continues to offer them up, say evolutionists, as we probe the depths of biology. ..."

And, oddly enough, almost invariably, the purported proofs of evolutionism are reported with such phrases as, “For the first time, scientists have observed ‘evolution’ …” and/or “Requiring us to totally rethink ‘evolution,’ …”

"And, oddly enough, almost invariably, the purported proofs of evolutionism are reported with such phrases as, “For the first time, scientists have observed ‘evolution’ …” and/or “Requiring us to totally rethink ‘evolution,’ …” "

Oddly enough, when I Google those phrases, I get just a single hit, to a comment on UD made by someone named Ilíon.

====I'm not going to ask you what you mean when you refer to evolution as "religious;" I've already encountered the creationist tendency to characterize as "religious" any idea that contradicts their particular dogmas. If you're a geocentrist, heliocentric astronomy is a religous idea based on metaphysical assumptions that are not required by "true" science. If you insist that diseases are caused by demons, then the same is true of germ theory. I assume you're neither of those, so you are content to label merely common descent and natural selection as "religious" ideas.====

So when evolutionists say god would not have designed the nested hierarchy pattern that is not a religious claim?

Ilíon,In fact the actual situation is quite the opposite. The blog (UncommonDescent) CH posts on is well known for deleting comments, banning posters and generally behaving in a way that would lead you to believe they cannot bear free discussion of their ideas.

Hunter:Evolutionary theory is unlikely, but necessarily true, for the alternatives are both false and not allowed anyway.

This reminds me of a story by Ravi Zacharias, it goes something like this. There was a man who thought he is dead. He goes around telling everyone he is dead. His family thought that he was joking and he will snap out of it, but when it was apparent that he was serious they became concerned. They took him to see a doctor. The doctor showed him all sorts of data about physiology, heart and brain function but he was not convinced. Finally after hours of talking to the man the doctor convinced him that dead people don’t bleed. At the very moment that this man conceded that dead people don’t bleed the doctor took a needle that was in his pocket and plunged it into the man’s arm. The man stared at his bleeding arm and said, “Well, what do you know. Dead people do bleed after all.”

Cornelius Hunter: So when evolutionists say god would not have designed the nested hierarchy pattern that is not a religious claim?

What is means is that the complex pattern of the nested hierarchy can result from a natural process, divergence along uncrossed lines, so the hypothesis of direct intervention to create the pattern is superfluous.

Steven: I am not convinced that evolutionists expected that genomic "junk" would have no function.

This is because like other religious Darwinists you refuse to face the truth. Casey Luskin exposed the rewriting of history in his article under the section Will Darwinists Now try to Rewrite the History of Junk-DNA?***Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, "they are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?"***Read the rest of his article for more examples.

Still not convinced? Take a look at this posting from just about a month ago by the high priest of Darwinism in the temple of Darwinian dogma. Junk DNA is still junk***Personally, I fall into the "it's all junk" end of the spectrum. If almost all of these sequences are not conserved by evolution, and we haven't found a function for any of them yet, it's hard to see how the "none of it's junk" view can be maintained. There's also an absence of support for the intervening view, again because of a lack of evidence for actual utility. The genomes of closely related species have revealed very few genes added from non-coding DNA, and all of the structural RNA we've found has very specific sequence requirements. The all-junk view, in contrast, is consistent with current data.***

Steven: In contrast, evolutionary theory offers a simple, straightforward explanation of these features: pseudogenes are "broken" copies of the formerly functional genes they resemble; ERVs are inherited remnants of actual viruses that inserted themselves into ancestral sperm or eggs.

No it is not that straightforward. Like are Darwinian drones you presume that God must have design everything as optimal according to our perspective. Even you’ve acknowledge that our perspective might not be accurate, but even if it is accurate there is no reason to justify why all God designs must be optimal.

The problem for the religious Darwinists is that you refuse to face the fact the pseudogenes and ERV which you claim are necessarily the results of random evolution could in fact be design and are function gene segments.

You are wrong Joe. It is not that Zachriel does not understand nested hierarchies. I’ve tried to explain it to him many times in the past but rather he refuse to see for it might be the demise of his religious belief in Darwinism. Isn’t that right Zacho? :)

The problem with handwaving is that it adds nothing to the conversation.

In biology, the existence of the nested hierarchy means that we can draw correlations between traits; for instance, a lower jaw comprised of a single bone and heterodont dentition allows us to predict many other characteristics of the organism, including its maternal behavior.

Steve - As far as I can see, for example, evolutionary theory doesn't have much at all to say about how life originated, nor does it depend on any particular account of abiogenesis, so how can it make predictions that have been falsified?

Actually evolution is directly dependant upon abiogenesis. Abiogenesis is an absolute must for evolution to be positively accepted. If abiogenesis is false then obviously life came from outside this planet and you need to consider a God and then, as has been suggested by so many evolutionists on this site, all your science is completely undependable since you don't know if it's been tampered with by a higher being. So as you see, evolution needs abiogenesis.

Fil: Actually evolution is directly dependant upon abiogenesis. Abiogenesis is an absolute must for evolution to be positively accepted.

Actually, gravity is directly dependent upon the natural origin of the universe. A natural origin of the universe is an absolute must for gravity to be positively accepted. If the natural origin of the universe is false then obviously gravity came from outside this universe and you need to consider a God and then, as has been suggested by so many gravitationists, all your science is completely undependable since you don't know if it's been tampered with by a higher being. So as you see, gravity needs a natural origin of the universe.

TBYou said "The problem for the religious Darwinists is that you refuse to face the fact the pseudogenes and ERV which you claim are necessarily the results of random evolution could in fact be design and are function gene segments."

I can face the fact that they COULD be designed. That's easy. Anything is possible. Nothing is forbidden. But the trouble is that if you make a claim like that, it's for you to support that claim.

Here I find object A. Object A has no purpose that I can determine. To me it does not look designed. I will label it "purpose unknown - possibly none".

You claim that object A does in fact have a purpose. You claim that it was designed.

You cannot suggest a purpose for the object. You cannot say how or when or by whom it was designed.

You claim that object A does in fact have a purpose. You claim that it was designed. I can easily face that fact that what you claim may be true.

However I do not see what difference that makes to the label I apply, "purpose unknown - possibly none".

So what benefit does your insight "that it might have function" bring?

Joe G,I'd be interested to hear from you, in say a paragraph or two in your own words, why ERVs are not evidence for Common Ancestry.

I mean, I can throw a link at you with literally thousands of papers supporting evolution. And I'm sure a bright guy like you does not need a paragraph or two from me explaining why ERVs are evidence for Common Ancestry.

So, let's hear in your own words why ERVs are not evidence for Common Ancestry?

I'm sure everybody here would appreciate it. Or are one liners and throwaway comments all you've got?

Actually, gravity is directly dependent upon the natural origin of the universe. A natural origin of the universe is an absolute must for gravity to be positively accepted. If the natural origin of the universe is false then obviously gravity came from outside this universe and you need to consider a God and then, as has been suggested by so many gravitationists, all your science is completely undependable since you don't know if it's been tampered with by a higher being. So as you see, gravity needs a natural origin of the universe.

So your ship will fall off the edge of the Earth. Or something.

So if abiogenesis proves to be false and the Law of Biogenesis stands then where did the first life come from for evolution to work it's magic?

Saying that something has no known function so it must have come about through evolution sounds to me like a Darwinism of the gaps approach. We don't have a good design explanation, therefore it must have been evolution.

Fil: So if abiogenesis proves to be false and the Law of Biogenesis stands then where did the first life come from for evolution to work it's magic?

"Abiogenesis proves to be false" is much too vague to constitute a valid hypothesis. No one knows exactly how life began, but once it began, the evidence strongly indicates that afterwards it evolved through natural mechanisms.

So if no one knows how the universe began, then where did the matter come from for the Solar System to evolve?

No one knows exactly how the universe began, but once it began, the evidence strongly indicates that afterwards the Solar System evolved through natural mechanisms.

OM's evotardgasm:The thing you have to remember is that the origin of undirected chemical processes could not have been via undirected chemical processes as they only exist in man-made undirected chemical processes.

So if not being able to support your position makes you an intellectual coward then I guess you are an intellectual coward. After all, you are unable to support your position. You could have answered the question, can you name a single thing that there is "a good design explanation" for?, instead of turning the question around. But you did not. Therefore you have no answer, for if you did you would most certainly have given it. Therefore you are an intellectual coward by your own definition.

Fair enough. Case closed, as they say. Unless of course you can answer the question?

Then you should be able to answer the question, I know you've read it.

Can you name a single thing that there is "a good design explanation" for?

I said the evidence was on my blog...No, in fact you provided a link to "ERVs are not evidence for Common Ancestry" which is a page of opinion of other peoples work. By "whoIsYouCreator.com no less. Hardly unbiased?

Zacho: The problem with handwaving is that it adds nothing to the conversation.

Handwaving? How many times have I asked you to demonstrate that nest hierarchy is an exclusive necessity of Darwinian evolution? Just because you can put things into an organizational chart does not make it a random product of descent. If nest hierarchy is the natural outcome of Darwinian fairytales then why do you have so many anomalies? Can you show the hierarchical prediction and necessity from Pakicetus dentition to whale dentition? It is not a problem for Design theory.

teleological blog: How many times have I asked you to demonstrate that nest hierarchy is an exclusive necessity of Darwinian evolution?

The nested hierarchy is the natural consequence of divergence along uncrossed lineages. A designer is as much superfluous to this process as it is to making planets follow their orbits across the sky.

teleological blog: Just because you can put things into an organizational chart does not make it a random product of descent.

Are you denying the objective existence of the nested hierarchy? Assuming you are not, then we have the problem with the construction "random product of descent". Descent is not a random process. Offspring strongly resemble their parents. That's rather the point.

teleological blog: If nest hierarchy is the natural outcome of Darwinian fairytales then why do you have so many anomalies?

Because lines sometimes cross.

Cornelius Hunter: The complex pattern of the nested hierarchy can result from design, so the unlikely hypothesis of chance creation to create the pattern is superfluous.

Zacho: The nested hierarchy is the natural consequence of divergence along uncrossed lineages.

This is a organizational methodology not a scientific necessity.

Zacho: A designer is as much superfluous to this process as it is to making planets follow their orbits across the sky.

Is it too much to ask ID deniers to learn a little bit about the subject they are criticizing? Your comment is equivalent to saying a designer is superfluous to a Rube Goldberg machine.

Zacho: Offspring strongly resemble their parents. That's rather the point.

We are not talking about how much you look like your mama. We are talking about the empirical scientific evidence that necessitates the exclusive Darwinian nested hierarchy. Darwinists have never been able to provide a shred of reproducible evidence of how macroevolution occurred to form this nested hierarchy.

Zacho: Because lines sometimes cross.

What the heck kind of explanation is that? What determines the timing of the cross? Why does one feature have precedent over another? The problem is that Darwinists are religiously motivated to promote a prescribed dogma. You will take the data and shuffle it a way that fits your religious belief not what is reality.

So when evolutionists say god would not have designed the nested hierarchy pattern that is not a religious claim?

First, if (as ID theorists have frequently argued) the Designer is not automatically assumed to be God, suggestions, or even assertions, about the Designer's motives are not automatically religious assertions. They might be premature, or careless, or otherwise bad science, but if a Designer is a scientific idea, then conjectures, arguments, or inferences about His nature and motives are likewise scientific.

Second, again, I don't think the usual claim is that the Designer would not have designed in a nested hierarchy. It is that design gives us no reason to suppose He would.

In the absence of a hypothesis about the Designer's design philosophy, methods, and motives, we would assume that, e.g. differences in cytochrome-c would appear to be distributed randomly (this appearance might be a mistake on our part -- there might well be a perfectly good reason for the distribution of similarities and differences -- but in our ignorance of that reason we would see no comprehensible pattern). That this unexpected and inexplicable (by us) pattern would happen to so closely resemble the nested hierarchy implied by branching descent would be very unlikely.

On the common and minimal assumption of "common design for common function," I do not think we would expect to see, e.g. fruit-eating bats and fruit-eating birds with wings more like insect-eating bats and flightless birds, respectively, than like each other. Again, we would not expect a nested hierachy. On the assumption of meticulous and individual design, we would not expect to see, e.g. similar structures used for whale flippers and bat wings, and again would not expect a nested hierarchy.

The nested hierarchy is the natural consequence of divergence along uncrossed lineages.

I challenge you to provide a valid reference for that claim- talk origins is not a valid reference.

Zachriel's next line is part of that valid reference. Children resemble their parents because they inherit traits from their parents. The descendants of a breeding population a few generations later will closely resemble the ancestral population because they inherit the traits of that population.

Mutations alter those traits slightly, and natural selection favors some traits over others. More mutations accumulate (beneficial ones preserved and harmful ones deleted by natural selection) over time. As a result of this, distant relations will resemble one another less closely than close relations will. As descent branches, each branch inherits (with modifications) traits that were unique to the founding population of that branch. Each branch thus forms a group united by shared traits that are unique to that group (and each branch is divided into sub branches and belongs to a series of super-branches -- larger groups united by inheritance from more and more ancient ancestors).

This is the basic logic of how branching descent with modification and no "lateral inheritance" must work.

Offspring strongly resemble their parents.

That puts a damper on UCD.

THAT is rather the point.

Great-to-the-millionth grand-offspring rather less closely resemble their great-to-the-millionth grandparents, of course.

Known designers mix-and-match at will.

So does nature.

That is rather the whole point about transitional forms and all...

Zachriel's point is that, e.g. nothing would prevent a designer from putting feathers on bats, or equipping whales with horizontal flukes like those of a shark or ichthyosaur. But evolution can't equip bats with complex features that evolved in a different lineage after that lineage separated from the line leading to bats, nor can it ignore the up-and-down (rather than side-to-side) motion typical of galloping mammals when equipping whales for swimming.

ID claims to explain the origin of life. You point to objects where we know the origin already. Humans. And we also have living organisms and all their functioning systems...And the "good explanation" appears to be missing from your sentence. What is the "good explanation" that explains living organisms? It's "ID" you say? Well I can equally say it's "ABC 123" if I don't provide supporting evidence. ABC 123 is just as good an argument as "ID" the way you use it.

So much for the "Science of ID".

And as for the link to "who is your creator?" well it contains links peer-reviewed papers refuting the claim that ERVs are evidence for Common Ancestry.

This is simply untrue and you know it. If you want to prove me wrong, pick one of those papers and post the name of it here. Then explain in your own words why it says what you say it does.

I believe you cannot. Prove me wrong. I doubt you will. IOW you focus on the organiszation and not the science.

Very typical of an intellectual coward.Says the guy refusing to discuss his own position. Point out a single paper, say why is supports your position. And it's very relevant as the site you link to does contain peer reviewed papers but they've done no actual work themselves. All they've done is list a load of other peoples work then contorted the point of the paper until it seems to support their point of view. So far so standard for your type of person.

Steven J,Joe has his own private definition of "nested hierarchy" and thinks it somehow disproves common descent. The fact that the world disagrees with him does not bother Joe in the slightest, it's just another day in ID land.

One wonders why he does not write his alternative up into a paper, get it peer reviewed and submit it to one of the desperate ID journals.

"...ID claims to explain the origin of life. You point to objects where we know the origin already. Humans."

Please tell me how do we know the origin of these objects already, if the very first objective is to find out what caused it? Like most Darwinian minds you also don't have the capacity to discern a self referential argument.

It goes like this: "Humans created the Stonehenge, therefore we already knew humans created the Stonehenge."

No wonder you don't understand ID and maybe better so. Because, with this logical deficiencies, it is better you never do real science, like design detection.

MichaelPlease tell me how do we know the origin of these objects already, if the very first objective is to find out what caused it?

Humans are known to create such artifacts. Are you claiming that we don't know who created "Stonehenge, my cars, my house"?

Like most Darwinian minds you also don't have the capacity to discern a self referential argument.What argument would that be? The question I've been asking is "Can you name a single thing that there is "a good design explanation" for?"

So far the only answer that has been forthcoming is "Stonehenge, my cars, my house".

All made by humans. All irrelevant to ID and it's claim to explain the origin of life.

Give me an example of an object that ID has a good design explanation or admit that you cannot.

It goes like this: "Humans created the Stonehenge, therefore we already knew humans created the Stonehenge."ID claims to explain the origin of biological systems that were present before human beings came on the scene.

Go on then.

No wonder you don't understand ID and maybe better so. What's to understand? You can't name any objects that ID can explain the origin of, you can't actually make ID explain anything at all. So what good is it?

Because, with this logical deficiencies, it is better you never do real science, like design detection.

What, like forensic science or archeology? Yeah, because they all use ID methodology. NOT!

Give me an example of something that is explained by ID better then it is explained by evolution.

Now there is another very basic principle of science that you clearly don't understand.

Because there are logically any number of possible causes for a single observed effect(phenomenon), science NEVER claims that it knows EXACTLY what caused something. This is why science admit that the universe has a cause and create theories about such a cause based on properties that comport with laws of logic only. No need to know what caused the universe in advance or as an explanation bounded to the universe itself.

You suggest that the origin of life cannot be related to intelligence because humans are the only intelligent entity we know. That is just stupid. We don't know that only humans are intelligent, in fact a lot of things might be intelligent. The only thing we do know is how the effects, that was caused by human intelligence look. Therefore we can ONLY infer that the Stonehenge, your car, my car, life etc. has been caused by an intelligence that bares similarity to humans. Any truth claim beyond this is unsupported by science.

MichaelTherefore we can ONLY infer that the Stonehenge, your car, my car, life etc. has been caused by an intelligence that bares similarity to humans.So ID claims life was created by humans? That's a new argument.

Can you proof evolution to be an explanation of the origin of life?

Evolution does not claim to be able to explain the origin of the first self replicator. ID does. That's why I'm asking you for that explanation.

Show me the academic support for such a claim.

The book you link to is not academic support for your claim that life was created via ID. It's simply a book that somebody published, it's not been peer reviewed, it's not had it's claims tested.

I can write a book showing the origin of life to be Pink Unicorns. So what.

Got any papers published in a peer reviewed environment that explain how life was created via ID? Thought not.

We don't know that only humans are intelligent, in fact a lot of things might be intelligent.

Many things *might* be true. The trick is to work out which ones are supported by evidence. I'm not denying that many things might be intelligent, but until you provide some evidence of a non-human designer creating life then it's just your opinion and nothing more.

So, any actual academic work out there showing ID was involved in the creation of life or just a succession of tedious books that can make any outlandish claim without fear of being corrected?

There are many problems with that book, and as far as I know Meyer has never responded to them.

See here for more details

http://pandasthumb.org/archives/2004/08/meyers-hopeless-1.html

Meyer argues that “many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins” (p. 218). He makes statements to this effect throughout the paper. Meyer does not say who these scientists are, and in particular does not say whether or not any of them are biologists. The origin of new genes and proteins is actually a common, fairly trivial event, well-known to anyone who spends a modicum of effort investigating the scientific literature. The evolution of new genes has been observed in the lab, in the wild, inferred in great detail between closely-related modern species, and reconstructed in hundreds of cases by comparing the genomes from organisms sequenced in genome projects over the last decade (see Long 2001 and related articles, and below).

And so on. And this is the best you've got! It must be otherwise you'd have provided that link instead.

Meyer is also at odds with another ID proponent, Behe. So who's right? Behe or Meyer?

There are a large number of documented cases of the evolutionary origin of new genes (again, a sample is here). We challenge Meyer to explain why he didn’t include them, or anything like them, in his review. We invite readers to wait to see whether or not Meyer ever addresses them at a later date and whether he can bring himself to admit that his most common, most frequent, and most central assertion in his paper is wildly incorrect and widely known to be so in the scientific literature. These points should not be controversial: even Michael Behe, the leading IDist and author of Darwin’s Black Box, admits that novel genes can evolve: “Antibiotics and pesticide resistance, antifreeze proteins in fish and plants, and more may indeed be explained by a Darwinian mechanism.” (Behe 2004, p. 356)

Michael,We invite readers to wait to see whether or not Meyer ever addresses them at a later date and whether he can bring himself to admit that his most common, most frequent, and most central assertion in his paper is wildly incorrect and widely known to be so in the scientific literature.Is that wrong? Why? Will you defend Meyer or just claim he's right and that's that? Is Meyer's central assertion right or wrong according to *you*?

Michael,Can you name a single thing that there is "a good design explanation" for?

And of course, providing that good design explanation would net you bonus points, rather then just claiming (as is typical for ID supporters) that it exists but for some reason you are unable to provide it (Joe G's SOP).

teleological blog, there was just one question in our last reply. Let's see how you answer it.

Zachriel: The nested hierarchy is the natural consequence of divergence along uncrossed lineages.

teleological blog: This is a organizational methodology not a scientific necessity.

That is incorrect. It is a direct (mathematical) consequence of grouping by ancestry. We can discuss the pattern traits make, given descent with modification, but we should resolve this beforehand.

Zachriel: A designer is as much superfluous to this process as it is to making planets follow their orbits across the sky.

teleological blog: Is it too much to ask ID deniers to learn a little bit about the subject they are criticizing? Your comment is equivalent to saying a designer is superfluous to a Rube Goldberg machine.

Is it too much for IDers to understand and respond to simple analogies. The movement of the planets is not a Rube Goldberg machine, but a consequence of the collapse of a primordial nebula. Unless you are now claiming that the Solar System was designed with its current orbital configurations.

teleological blog: Just because you can put things into an organizational chart does not make it a random product of descent.

Zachriel: Offspring strongly resemble their parents. That's rather the point.

teleological blog: We are not talking about how much you look like your mama. We are talking about the empirical scientific evidence that necessitates the exclusive Darwinian nested hierarchy.

You seem to have trouble following a line of thought. You used the phrase "random product of descent" (which you snipped). But descent is not random!

teleological blog: Darwinists have never been able to provide a shred of reproducible evidence of how macroevolution occurred to form this nested hierarchy.

We would be happy to step you through the evidence. We have to establish a few mathematical concepts; first, the offspring of descent along uncrossed lines form a nested hierarchy *when grouped by ancestry*. This is not an empirical result, but a mathematical necessity.

We asked just one question, which you didn't respond to: Are you denying the objective existence of the nested hierarchy?

But www.whoisyourcreator.com is in fact a valid reference? Yes, indeed. As that's what you gave me earlier in support of your "argument" that you can't even recap in your own words (i.e. you don't understand it and it's just a c+p).

It must be easy to support your position when you can simply dismiss inconvenient evidence with a claim of "that's not a valid reference".

I guess those 65,000 papers I linked to at Nature are also invalid references?

I guess there's only one valid reference for you right Joe? And that's the Bible. Or the Koran, depending on what personality has control, right Joe?

I trust that you have relinquished your stupid notion that only human intelligence can be detected. If you don't, do you imply that the SETI has to end their activities on your command.

One general comment on your arguments against Meyer's book. Don't confuse origin of life with genetic variation in pre-existing life.

How can Behe's comment (from 2004) be at odds with Meyer's claim about the origin of life if Behe's comment is about variation in pre-existing life?

You see most anti-ID people create their own dilemmas and argue them.

Meyer is very clear that his argument is about the origin of life. It is just funny to listen to the unwarranted extrapolations from existing life to the origin of life.

Your blabbing about Meyer's book not being peer reviewed is called the the fallacy of appeal to authority. It does not matter if his book were first found in prehistoric cave writings you need to argue the arguments. There are more than enough academics that agree on its academic credentials.

Oh Michael, where are those probability calculations you keep bragging about? The ones that supposedly prove ID?

Looks like you got caught with your rhetorical pants around your ankles again.

BTW, the Meyer paper wasn't peer reviewed. It was disavowed by the journal in which it was published because it was pushed through by a dishonest editor without undergoing the proper peer review process.

MichaelI trust that you have relinquished your stupid notion that only human intelligence can be detected.

I never said that. I'm simply pointing out that you've never provided evidence for any creative intelligence other then humans, but somehow expect me to agree that it exists.

If you don't, do you imply that the SETI has to end their activities on your command.

They, unlike you, are looking.

Your blabbing about Meyer's book not being peer reviewed is called the the fallacy of appeal to authority.

That would be true if as well as ID supporting books there were ID supporting peer reviewed papers. There are plenty of both that support evolution. But only books that support ID.

It does not matter if his book were first found in prehistoric cave writings you need to argue the arguments.

As per that link to the review on Pandas that's already been done. You just have to read it. I can't make you do that.

There are more than enough academics that agree on its academic credentials.

A list please. And your list will carry more weight if those academics are not affiliated with ID already, e.g. members of the Discovery Institute.

You are certainly not a trustworthy witness to anything important from what I have seen.

Interesting how you don't address a single point raised in the review, despite me copying a few here for you to read.

P.S.Here is another peer reviewed example of ID being a better explanation for large body plans:

http://en.wikipedia.org/wiki/Sternberg_peer_review_controversy

It actually describe and evaluate all the evolutionary propositions and conclude ID based on a well known scientific method, called best explanation.

Why don't you summarize the conclusions of that paper in your own words?

And somehow I don't think that a paper a few thousand words long "actually describes and evaluates all the evolutionary propositions". If you think it does, then you are in error.

The conclusion of that "paper" is

An experience-based analysis of the causal powers of various explanatory hypotheses suggests purposive or intelligent design as a causally adequate--and perhaps the most causally adequate--explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent. For this reason, recent scientific interest in the design hypothesis is unlikely to abate as biologists continue to wrestle with the problem of the origination of biological form and the higher taxa.No explanation of any mechanism, any specific time that intervention happened.

I could suggest that Pink Unicorns did it, and be supported by the same level of evidence that Meyer provides.

Evolutionists have accommodated the observations in nature of the so-called Nested Hierarchy of species. Of course, when features are unexpected and do not fit into a nested structure, like cusped teeth in fish, that is not a problem for evolution either.

Again and again, evolutionists are great at accommodating observations and hyping it as evidence for a theory that was supposedly settled a hundred years ago. Yet, does anyone really believe that if nested hierarchies were not found this would falisify the theory?

Evolutionists use great rhetoric to have most of the evidence BOTH ways....

They make an observation in nature and then paint the target circles around the observation and claim victory. If they observe a contradiction to the first expectation, then they paint target circles around that too and claim victory again. New fossils are hyped on the front page as the missing link before they are demoted with a lot less fanfare on page 36D in 6 point font. Then next year another candidate becomes the front page missing link to be demoted later, and so the cycle goes on and on.

A good theory is supposed to be about making accurate prediction ahead of time, measuring those predictions, and honestly looking at contradictions to the theory.

Certainly all the mysticism around the powers attributed to Natural Selection are giving many biologists pause to be skeptical.

MichaelYou disregard the ability to detect the act of intelligence in the origin of life, but you accept the SETI's effort might achieve its goal.

You have not detected intelligence in the origin of life. Have you? If you have, tell me a single thing about that intelligence.....

Let us look at your generalization and lying.

Yes, lets.

I can not make a selection...so just go here and see who are actually endorsing Meyer's book.Yes, that site is hosted by the Discovery Institute. Hardly partisan. So, to be clear, you send me to a site that is selling the book in order to establish it's credentials? Got anything a bit more independent perhaps?

Hardly. If we look at the articles listed we see that the total number of articles published since 2005 is…hold your breath…ONE! That single article is authored by our old friends, William A. Dembski and Robert J. Marks II. It is also mentioned in the previous resource – Evolutionary Informatics Lab. If we don’t count that article twice, then there are NO articles published since 2005.

A final list of published "ID friendly" articles can be found at http://biologicinstitute.org/research/

There are a total of 28 articles listed, going back to 1993. On average that’s less than two per year. ALL of the articles listed are from non-ID journals. They include the articles listed by the other ID references. At that site we see that the total articles published in either 2009 or 2010 is ZERO.

Moreover if you read the abstracts for the articles you see that any references to ID are nonexistent. From http://carumbasblog.blogspot.com/2010/05/id-science-journals.html

Have a nice life wallowing in your delusions of reality.

Indeed. And you keep believing that a few papers that claim (but don't actually) support ID trumps 65,000 thousand papers that actually do support evolution.

NealA good theory is supposed to be about making accurate prediction ahead of time, measuring those predictions, and honestly looking at contradictions to the theory.

Presumably you think ID is such a theory. Can you give us a few examples of accurate ID predictions made ahead of time, measuring those ID predictions and honestly looking at contradictions to the theory of ID?

NealOf course, when features are unexpected and do not fit into a nested structure, like cusped teeth in fish, that is not a problem for evolution either.

Citation please. And what is the ID explanation for "cusped teeth in fish"? Oh, that's right. You don't have one. You just *know* it exists and whatever it is it's better then the Darwinian explanation.

Evolutionary biology has not yet provided an explanation of the evolution of teeth and cusps. Two controversial hypothetical models, the field model [36] and the clone model [37], have been proposed. The field model postulates that heterodonty is due to graded values of hypothetical morphogens [36, 38]. In this model, each dental quadrant is divided into three subfields: incisors (key tooth, 1st, mesial incisor), canines, and molariforms (key tooth, 1st, mesial molar). Each tooth develops according to its position in the field. Teeth belonging to the same field have graded similarities according to the distance from the field origin: the third human molars, which generally develop later but disappear earlier than the other molars, are the most variable since they are at a position in which the morphogenetic field is weak. This model further suggests that multicuspid teeth of mammals derive their evolutionary origin from the union of many single reptilian tooth germs [39]. It is speculated that the signals that were used in our ancestors to develop each tooth separately were combined in modern species to create a single tooth with a more complicated morphology. Each tooth cusp evolved independently under specific genetic control, and the same sets of genes function for all cusps; thus, a reaction-diffusion mechanism may underlie the activation of genes at specific locations and times to create the crown patterns [5, 39].

What model has ID proposed to explain cusps?

Oh, that's right. ID does not explain anything. It just points out gaps in the Darwinian models.

Prove me wrong. What is the ID theory regarding the origin of teeth? Is it "the designer designed teeth because he wanted his designs to have teeth - design is a mechanism you know"?

OM ... who gives every indication of being a fool (that is, intellectually dishonest), and a silly one at that: "What model has ID proposed to explain cusps? .Oh, that's right. ID does not explain anything. It just points out gaps in the Darwinian models..Prove me wrong. ..."

It it *really* necessary to explain the horrendous logic on display here (*)? The question-begging? The special-pleading? The argumentation from ignorance? The argumentation from (asserted) authority? The argumentation from (asserted) privledge? The anti-scientific, and worse, anti-logical, hypothesis-protection?

EVEN IF it were true that all ID does is point out the gaps (**) in Darwinism, that is enough: Darwinism fails, and only the foolish/dishonest ideologues are holding onto it in the face of its so blatant, multi-level inadequacy.

(*) Do DarwinDefenders know any other kind? Seriously, do they? I've never seen evidence of it.

Ilíon,Is it *really* necessary to explain the horrendous logic on display here (*)? The question-begging? The special-pleading? The argumentation from ignorance? The argumentation from (asserted) authority? The argumentation from (asserted) privledge? The anti-scientific, and worse, anti-logical, hypothesis-protection?

I think only some members of the ID community fit your description. Some are quite honest in their dealings.

EVEN IF it were true that all ID does is point out the gaps (**) in Darwinism, that is enough: Darwinism fails, and only the foolish/dishonest ideologues are holding onto it in the face of its so blatant, multi-level inadequacy.

In fact that's incorrect. Darwinism, with all it's faults will stand until something comes along that explains the evidence better.

Did people stop using Newtons laws once it became obvious the did not explain everything? No, they only stopped using them when a better idea came along. Until that better idea comes along Darwinism is here to stay.

Neal,The mantra of evolutionists that makes their theory a settled fact

That's how science works. I realize it's a new idea to some around here. And anyway, science does not "prove" things. Proof only exists in Mathematics. Science provides tentative explanations that may or may not be ultimately overturned. The only unfixed, unmoving explanations to be have come from theists who have the answers direct from the man upstairs. They never change because they don't need to and people cling to them because of it.

So what happens to the theory of evolution when genetic differences between species that have been "nested" by evolutionists are so great that they could not be closely related in evolutionary terms? Another example of convergence? Of course, convergence is not a problem for evolutionists either, since it accommodated that too. Talk about talking lemons and making lemonade. As far as being creative in making up great just so stories, rhetoric, and getting skeptics to believe they have to disprove a negative... evolutionists reign as champs. Posterity will say otherwise.

Neal Tedford: So what happens to the theory of evolution when genetic differences between species that have been "nested" by evolutionists are so great that they could not be closely related in evolutionary terms?

Are you claiming that the nested hierarchy of biological traits is not strongly supported?

Neal Tedford: Evolution has weaned off the speculation bottle for 150 years. It's time for the dog to hunt or be retired.

Speculation is an important component of the scientific method. However, speculation is not a conclusion, but just the first step in forming a hypothesis.

Neal,So what happens to the theory of evolution when genetic differences between species that have been "nested" by evolutionists are so great that they could not be closely related in evolutionary terms?

Citation please.

Another example of convergence? Of course, convergence is not a problem for evolutionists either, since it accommodated that too.

Why is convergent evolution a particular problem for evolution?

As far as being creative in making up great just so stories, rhetoric, and getting skeptics to believe they have to disprove a negative...

All you have to do to prove your point is show how ID explains something better then the Darwinian alternative does.

ID is nothing but a big just so story. I guess 65,000 papers supporting evolution is irrelevant to you. More "just so" stories.

evolutionists reign as champs. Posterity will say otherwise.

People have been making that claim for over 162 years

http://chem.tufts.edu/AnswersInScience/demise.html

What specifically makes you think posterity will say otherwise?

Tell me Neal, what is your predicted date for the fall of Darwinism? Do tell, and I'll see If I can add it to the list

Neil,Evolution has weaned off the speculation bottle for 150 years. It's time for the dog to hunt or be retired. And all you have to do to make that happen is to provide a better explanation for the things that evolution explains.

The genetic differences aren't ""nested" by evolutionists," the nested hierarchy is the actual data described mathematically. This is why your side constantly violates the Ninth Commandment by describing this as mere "similarity."

These nested hierarchies can be observed by anyone on the Web, using public-domain sequencing data and public-domain computer programs. You have no excuse other than your own dishonesty for not examining the actual data for yourself.

"... are so great that they could not be closely related in evolutionary terms?"

But they aren't, which is the problem for you, which is why your side does nothing but lie.

These relationships span phyla. In case you are so aggressively ignorant that you don't know what that means, the relationship between you and yeast is obvious from them.

And it's the pattern of differences we're talking about, so pretending that it's just "similarity" is a LIE.

"Another example of convergence?"

No, DIvergence. Differences. You can't explain them, so you lie through your teeth.

"Of course, convergence is not a problem for evolutionists either, since it accommodated that too. Talk about talking lemons and making lemonade. As far as being creative in making up great just so stories, rhetoric, and getting skeptics to believe they have to disprove a negative... evolutionists reign as champs."

How would you know, Pastor Neal? You just continue to bear false witness. You're afraid to look for the truth.

Zacho: Nested hierarchies are defined in terms of sets. Can a set be an element of another set?

Not in cladistics.

teleological blog: This is a organizational methodology not a scientific necessity.

Zacho: That is incorrect. It is a direct (mathematical) consequence of grouping by ancestry. We can discuss the pattern traits make, given descent with modification, but we should resolve this beforehand.

You are the one that is incorrect. Mathematic probabilities of trait patterns are based on the assumption of Darwinian descent which by the way the same probabilities can be used to calculate design patterns. But the real problem is your hierarchy is based on a predefined pattern of descent. e.g. You are not going to take all the known taxa and throw them in a pot and calculate based on some probability and see what comes out? I guarantee you will not get the same tree you have now. So much for your objective nested hierarchical fantasy.

You still have not shown why I cannot build a nested hierarchy based on design. Any intellectually impaired Darwinists can make up a ridiculous classification system but that does not mean that a rational and logical classification of known taxa cannot be created based on design. The Linnaean system based on design work pretty well until the Darwinists decided to adopt it for their twisted fairytale and it is by and large still used. As a matter of fact it was Linnaean’s hierarchical nature the Darwinian Priors adopted to promote their fairytales.

Zacho: The movement of the planets is not a Rube Goldberg machine, but a consequence of the collapse of a primordial nebula. Unless you are now claiming that the Solar System was designed with its current orbital configurations.

Is it too much for ID deniers to understand how analogies work? Must you be so narrow focused? Our solar system and universe is analogous to a Rube Goldberg system in that the laws of physics are fine tuned. Our planets follow their orbits because the gravitational coupling constant is precisely tuned. If the fine structure constants are slightly different the fundamental forces would be altered and stars may never form. Yes even the sun-earth-moon system is finely tuned, in terms of age, location, surface gravity.

Zacho: You used the phrase "random product of descent" (which you snipped). But descent is not random!

You descended from your mama is not random but your descent from your chimpy uncle well that is another story. The fairytale that new species arise based on RM&NS is a random process makes the product random. i.e. When your mama gave birth there is every expectation that the baby would be a human being. However, in your fairytale a human being is not the expected outcome of your chimpy uncle. IOW, there is no way of knowing a human being would eventually be the out come of an ape.

Zacho: We would be happy to step you through the evidence.

I seriously doubt it. I’ve waited as long as I can remember for this imaginary evidence.

Zacho: We asked just one question, which you didn't respond to: Are you denying the objective existence of the nested hierarchy?

Absolutely, if you deny the objective existence of the Linnaean design hierarchy.

TB,You still have not shown why I cannot build a nested hierarchy based on design.

You can. Please do so! It might help support the claims of ID!

You descended from your mama is not random but your descent from your chimpy uncle well that is another story. The fairytale that new species arise based on RM&NS is a random process makes the product random. i.e. When your mama gave birth there is every expectation that the baby would be a human being. However, in your fairytale a human being is not the expected outcome of your chimpy uncle. IOW, there is no way of knowing a human being would eventually be the out come of an ape.

Vehicles can be aggrainged in a nested hierarchy based on charateristics. There's car, mini-vans, SUV's, truck, etc. Then we've got boats, airplanes, etc. And they were all designed. They form a hierarchy (please correct me if I'm wrong) because engineering, manufacturing, and economic factors place constraints on design.

As humans can choose to implement designs in any way there can be configurations in such a hierarchy that are impossible for evolution to achieve.

For example, an innovation (echolocation, the CD player) can pass only to the organisms descendants in biology but for vehicles once the CD player exists it can appear in all vehicle types at once, even seemingly unrelated ones (cars, boats)

Evolution cannot make echolocation available in the same way.

A significant difference I hope you'll agree.

And while horizontal gene flow causes some of the hierarchy to be less clear cut I believe that's less of an issue the further down the tree you go.

Have a look at this

http://www.ncbi.nlm.nih.gov/pubmed/19271179

We describe the reasons why the newly recognized process of horizontal gene transfer (HGT) forces evolutionists who study classification and microbiology to go beyond the classical Darwinian framework. We recall the importance of processes in philosophical definitions of species and for taxonomical purposes in general. More precisely, we present a brief description of a possible transition from a thinking inspired by essentialism to eliminative pluralism in the species debate and we insist on a major philosophical lesson: that processes matter and that, consequently, HGT cannot be overlooked in microbial classification. We then expand the conclusions of eliminative pluralism to microbial classification, namely (i) that species are not real and (ii) that overlapping taxonomies are equally legitimate when they are based on real natural processes. We introduce alternatives to the traditional species concept and describe what we call evolutionary units. Two types of units can be described: coherent and composite. The former are sets of co-evolving genes, pathways, or organisms, which share the same phylogenetic origin, while the latter comprise genes, pathways, or organisms with component parts from multiple phylogenetic origins. These evolutionary units are either "mostly flexible" or "mostly rigid" in their genetic composition and we discuss how this dissimilarity could profoundly affect our systematics practice. In this chapter, we illustrate how much there is to learn from the reconstruction of the complex evolutionary histories of all evolutionary units - large or small - by giving up the notion of species for recombining microbes, and suggest replacing a unique nested hierarchy of life with a comprehensive database including overlapping taxonomical groups.

teleological blog: How many times have I asked you to demonstrate that nest hierarchy is an exclusive necessity of Darwinian evolution?

As you have asked, you should be willing to follow the argument. Stop at any point where you have a question or objection, but try not to jump ahead.

Zachriel: Nested hierarchies are defined in terms of sets. Can a set be an element of another set?

teleological blog: Not in cladistics.

Mammals is a set contained within the set of vertebrates.

Zachriel: The nested hierarchy is the natural consequence of divergence along uncrossed lineages.

Zachriel: It is a direct (mathematical) consequence of grouping by ancestry. We can discuss the pattern traits make, given descent with modification, but we should resolve this beforehand.

teleological blog: Mathematic probabilities of trait patterns are based on the assumption of Darwinian descent which by the way the same probabilities can be used to calculate design patterns.

We're not talking about traits, but the mathematical pattern of descent along uncrossed lines when *grouped by ancestry*. We will discuss traits once we are clear on this.

teleological blog: But the real problem is your hierarchy is based on a predefined pattern of descent. e.g. You are not going to take all the known taxa and throw them in a pot and calculate based on some probability and see what comes out?

Actually, that is how cladistics works. You take a large number of traits, and create a large number of possible trees with their entailed predictions, then find the one that fits the data most parsimoniously.

teleological blog: You still have not shown why I cannot build a nested hierarchy based on design.

Of course you can.

teleological blog: Any intellectually impaired Darwinists can make up a ridiculous classification system ...

The nested hierarchy of taxonomic traits is an empirical observation. Please be specific. Are you denying that there is a nested hierarchy of taxonomic traits for most taxa?

teleological blog: Yes even the sun-earth-moon system is finely tuned, in terms of age, location, surface gravity.

We have a great deal of evidence that solar systems form naturally. We can even see stars in various stages of their formation, and have in the last few years, even detected planets.

teleological blog: You descended from your mama is not random but your descent from your chimpy uncle well that is another story.

Human and chimpanzees share far more similarities than they have differences.

Zachriel: Are you denying the objective existence of the nested hierarchy?

teleological blog: Absolutely, if you deny the objective existence of the Linnaean design hierarchy.

Evolutionists as a whole are not open to skepticism. The design inference is ignored by the evolutionist.

All digital information systems are known to have an intelligent origin. Purely natural processes are incapable originating digital information. The living cell is a complex digital information system and network. Therefore, the best explanation for the origin of the living cell is from an intelligent being.

You can rant, scream, call names, but lets cut threw all the smoke of a million half-baked evolutionary arguments and empirically see and accept that digital information cannot be a product of purely natural and unaided natural processes.

Natural Selection sounds like a great scientific word, but the mystic powers it is given to change, equip, and engineer life (terms evolutionists have used) is a kind of science-like vodoo.

I mean, St Nickolas was a real man, but Santa Claus is an exaggeration of his life. So too, natural selection occurs to some degree but evolutionists have made it into some kind of natures Santa Claus.

So here's the challenge. Show me one example in nature of a digital information system originating without the aid of intelligence? If you can not provide an example then please accept ID as a better explanation of the origin of life.

Not at all. Don't forget it used to be the status quo. Until recently design was the explanation for everything, remember?

All digital information systems are known to have an intelligent origin.

This one? Ok. You realise that this logically ends up with humans having designed humans right? Purely natural processes are incapable originating digital information.

And your proof of that is what, exactly? That you think it's true? You really don't know how science works at all do you?

The living cell is a complex digital information system and network.

Therefore ID, right?

Therefore, the best explanation for the origin of the living cell is from an intelligent being. Ah, yes, Therefore ID.

You can rant, scream, call names, but lets cut threw all the smoke of a million half-baked evolutionary arguments and empirically see and accept that digital information cannot be a product of purely natural and unaided natural processes.

Yes, because you said so. I'm afraid I'll need a little more then that to be convinced.

Natural Selection sounds like a great scientific word, but the mystic powers it is given to change, equip, and engineer life (terms evolutionists have used) is a kind of science-like vodoo.

Sounds more like ID to me to be honest. ID can explain anything, evolution not so much.

I mean, St Nickolas was a real man, but Santa Claus is an exaggeration of his life. So too, natural selection occurs to some degree but evolutionists have made it into some kind of natures Santa Claus.

Only because you lot have failed to come up with a better explanation. Explain the observed data better then evolution and you win! It's as simple as that!

So here's the challenge. Show me one example in nature of a digital information system originating without the aid of intelligence?

Biological life on planet earth.

If you can not provide an example then please accept ID as a better explanation of the origin of life.

For the sake of argument let's say that I accept Jesus into my heart, er, I mean I accept ID as a better explanation of the origin of life.

Now, what is that explanation, specifically? Or is that it? That "ID is the explanation of the origin of life".

I mean, what's the explanation then? Some specific details, mechanisms, when, who how. You know, all that "science" stuff. Got any of it? Or is your claim that "ID is a better explanation of the origin of life" the sum total of how ID explains the origin of life?

Zachriel:Actually, that is how cladistics works. You take a large number of traits, and create a large number of possible trees with their entailed predictions, then find the one that fits the data most parsimoniously.

Funny that is exactly what I have been saying.

Yet oleg kept saying I am wrong.

We have a great deal of evidence that solar systems form naturally.

You don't have any evidence that our solar system formed via blind, undirected processes.

Michael,The thing is Darwinists are so dense they block out the consequences of these null hypotheses not being disproved.

And what consequences would those be, exactly?

And if those Darwinists are so dense, how come Darwinism is taught in every secular university, in every country in the world? How come every court case involving ID is lost to the dense Darwinists?

How come those dense Darwinists seem to win every battle they fight with ID? How come they make up 99%+ of all working biologists?

You are insulting many thousands of people who dedicate their working lives to improving our understanding of nature.

Other reasons why that paper is pure bunk are discussed here.

http://all-too-common-dissent.blogspot.com/

This covers the main points

Their 2004 paper contains this as a premise:

"How did inanimate nature write:1. the conceptual instructions needed to organize metabolism?2. a language operating system needed to symbolically represent, record andreplicate those instructions?3. a bijective coding scheme (a one-to-one correspondence of symbolmeaning) with planned redundancy so as to reduce noise pollution between tripletcodon "block code" symbols (bytes) and amino acid symbols?... "

Fails from the get go.They start by assuming their conclusion - thatmetabolism/genetic code was pre-planned and written, and that "inanimate nature"cannot do this.Theirs is an argument via analogy combined with an argument via defintioncombined with an argument via personal incredulity, gussied up with somesuperfluous jargon and 'information theory' gibberish.

What about this peer reviewed scientific paper:Natural selection as theprocess of accumulating genetic information in adaptive evolutionM.KimuraGenetical Research (1961), 2:127-140 Cambridge University Press

I should also note the last sentence of the liked paper:"We invite potential collaborators to join us in our active pursuit of falsificationof these null hypotheses."In other words, they've just tossed out some hypotheses. Which is fine. What is not fine is that their acolytes then proceed to present these hypotheses as some sort of unfalsifiable truths.

Note the last sentence.

What is not fine is that their acolytes then proceed to present these hypotheses as some sort of unfalsifiable truths.

Which makes your last sentence

The thing is Darwinists are so dense they block out the consequences of these null hypotheses not being disproved.

Very silly indeed.

So, tell me, what are the terrible consequences of these null hypotheses not being disproved? Be as specific as you can now!

Nat wrote:"Vehicles can be aggrainged in a nested hierarchy based on charateristics."

They can be arranged in MANY nested hierarchies based on characteristics. That's the problem you have to explain.

For living organisms, ONLY ONE nested hierarchy fits. Moreover, the nested hierarchy that fits the organisms can be superimposed on the hierarchies of virtually every one of their parts, which we all know is completely false for vehicles.

If you disagree, tell me how the 1994-2002 Honda Pilot (a simply rebadged Isuzu Rodeo) and its parts fit only a single nested hierarchy.

"There's car, mini-vans, SUV's, truck, etc."

Yes, and many completely identical parts are shared among them. That's not true for living things—you can't explain the differences, so your side lies and pretends that it's just "similarity"

"Then we've got boats, airplanes, etc. And they were all designed."

They all fit multiple hierarchies.

"They form a hierarchy (please correct me if I'm wrong)"

You're wrong. You can construct many different hierarchies depending on the characteristics you score.

"... because engineering, manufacturing, and economic factors place constraints on design."

But their component parts don't fit the same hierarchy. That's because of constraints from common descent.

Even when humans explicitly set out to design strict nested hierarchies (military commands) they have to put in exceptions to make them work.

I said:The thing is Darwinists are so dense they block out the consequences of these null hypotheses not being disproved.

OM said:"And what consequences would those be, exactly?"

My point exactly, so you admit that you are too dense to see the consequences for yourself.

Let me use the words of my favorite evolutionist to help the struggling Darwinists:

"The existence of a genome and the genetic code divides living organisms from nonliving matter. There is nothing in the physicochemicalworld that remotely resembles reactions being determined by a sequence and codes between sequences." Yockey 2005

We've been through this before with the meaning of digital and the cell. Parallels can be drawn between quaternary numbers and the way genetic code is represented by DNA. The four DNA nucleotides abbreviated A, C, G and T can represent the quaternary digits in numerical order 0, 1, 2, and 3.

The nucleotide sequence GATTACA can be represented by the quaternary number 2033010.

Digital can mean more than electronic signals. The digital nature of DNA is more than a metaphor. DNA is much more complex than an electronic computer because it's code is capable of directing the reproduction of additional cell units.

Think of it this way... written text in a book is considered digital because it is formed by discrete letters of the alphabet. The digital informational property is simply in the chemicals of the ink on the paper, it is in the information that is communicated via the letters. The chemicals of the ink do not dictate the arrangement of a work of Shakespeare and more than the chemicals of DNA dictate the information that is stored in the DNA.

Smokey, to deny the digital nature of dna is to deny what even your fellow evolutionists write....

I should have said that the digital information property IS NOT simply in the chemical s of the ink on the paper.

Books and articles need authors (intelligence. The ink does not form letters and great works of literature by some chemical property that causes the ink to form automatically and naturally. But this is exactly what evolutionists are claiming that DNA does even though it is more complex and integrated information than a work of Shakespeare. Go figure.

We're open to informed criticism, just not the ignorant hot air and empty bluster of fools like you.

The design inference is ignored by the evolutionist.

Because there's no evidence for it.

All digital information systems are known to have an intelligent origin. Purely natural processes are incapable originating digital information. The living cell is a complex digital information system and network. Therefore, the best explanation for the origin of the living cell is from an intelligent being.

Same dishonest equivocation over the term "digital". check

You can rant, scream, call names, but lets cut threw all the smoke of a million half-baked evolutionary arguments and empirically see and accept that digital information cannot be a product of purely natural and unaided natural processes.

And you can post all the foolish nonsense on backwater IDiots sites you want, it won't affect scientific reality one iota.

Natural Selection sounds like a great scientific word, but the mystic powers it is given to change, equip, and engineer life (terms evolutionists have used) is a kind of science-like vodoo.

It only seems like voodoo to ignorant dolts like you who haven't studied it and don't have the faintest idea how it actually works.

So here's the challenge. Show me one example in nature of a digital information system originating without the aid of intelligence? If you can not provide an example then please accept ID as a better explanation of the origin of life.

I already gave you one. The pond that forms in my back yard every winter creates a digital record of the evening's temperature: frozen = below 32F, non-frozen=above 32F.

Pastor Neal continues to violate the Ninth Commandment:"Books and articles need authors (intelligence. The ink does not form letters and great works of literature by some chemical property that causes the ink to form automatically and naturally. But this is exactly what evolutionists are claiming that DNA does even though it is more complex and integrated information than a work of Shakespeare. Go figure."

Why is it that working biologists and biochemists have replicated every (metaphorically) digital information transfer step with purified enzymes in vitro, Pastor Neal?

Books and articles need authors (intelligence. The ink does not form letters and great works of literature by some chemical property that causes the ink to form automatically and naturally. But this is exactly what evolutionists are claiming that DNA does even though it is more complex and integrated information than a work of Shakespeare. Go figure

It has been demonstrated many times over that iterative processes involving imperfect replicators filtered by selection can and do produce increased complexity.

Please provide the justification for your assertion that "complexity" must equal "consciously designed".

Still waiting for that proof the evolution is mathematically impossible you claimed, but it's obvious you were lying. Again.

Let me use the words of my favorite evolutionist to help the struggling Darwinists:

"The existence of a genome and the genetic code divides living organisms from nonliving matter. There is nothing in the physicochemicalworld that remotely resembles reactions being determined by a sequence and codes between sequences." Yockey 2005

"This post is written by Cynthia Yockey. The first thing I want noted about my father is that he is not in any way, shape or form a Creationist. He does not support Intelligent Design. He supports Darwin’s theory of evolution and points out that it is one of the best-supported theories in science."

So Yockey thinks you IDiots are full of it. You sure you want to use him to defend IDC?

Dr Yockey: "origin of life is unknowable... must be accepted as an axiom of biology.

Sooo, let's just throw up our hands and pretend that what we see wasn't designed.

How insane does it get???

The design inference does offer a reasoned and good explanation and your side wants to turn ignorance into a biological axiom. You guys are on the verge of being relegated to the same little island as the flat earth people if you keep it up.

You are completely right. The axiom is completely based in materialistic ignorance IOW - metaphysical commitment to materialism. Yockey's work made it abundantly clear that there are nothing in the physicochemical world that can account for the origin of information in the origin of life. As a committed materialist the only option at his disposal was to conclude that it is a physical unknowable.

That in itself is one of the strongest arguments against materialism that I know of. That is why Yockey stays my favorite evolutionist.

Yockey, has successfully proven that the origin of information can not have a physical explanation.

Anyone interested should read his work. He produced outstanding work explaining the application of information theory to genetic information. The world will always be indebted to him.

JoeYOU can't explain the differences beyond appealing to magical mystery mutationsWhy do you link to your own site as if it's relevant to anything we're talking about? You've already displayed a profound ignorance of what's being discussed and have shown that you have nothing to contribute beyond petty insults.

Your links to you own site are hardly authoritative are they? Yet you provide them as if expecting me to be convinced somehow by the tripe presented there as "science". Just not going to happen.

There is no evidence that demonstrates the genome and cell are reducible to blind, undirected chemical processes.

Yawn. Is this it Joe? For the rest of your life? Just going to repeat this one point over and over?

Michael. Yockey's work made it abundantly clear that there are nothing in the physicochemical world that can account for the origin of information in the origin of life.And he he says the opposite. It's amazing how you know his work better them him.

"We have detected the presence of anthracene molecules in a dense cloud in the direction of the star Cernis 52 in Perseus, about 700 light years from the Sun," explains Susana Iglesias Groth, the IAC researcher heading the study. In her opinion, the next step is to investigate the presence of amino acids. Hydrocarbon molecules like anthracene are essentially prebiotic, but when they are subjected to ultraviolet radiation in the presence of small inorganic molecules, such as water and ammonia, which can act as a source of oxygen and nitrogen, it is possible to yield amino acids and other compounds essential for the development of life. Groth worked with Rafael Rebolo of the Instituto Astrofísica de Canarias, David Lambert of the University of Texas, and others.

The presence of diffuse spectroscopic bands in the spectra of the interstellar medium has puzzled researchers since at least as early as the 1980s; there are hundreds of such bands. Their existence has hinted at the presence of small molecules in the interstellar medium, but many of those bands have remained unassigned.

"Two years ago," adds Iglesias, "we found proof of the existence of another organic molecule, naphthalene, in the same place, so everything indicates that we have discovered a star formation region rich in prebiotic chemistry." Until now, anthracene had been detected only in meteorites and never in the interstellar medium. Oxidized forms of this molecule are common in living systems and are biochemically active. The new finding suggests that a good part of the key components in terrestrial prebiotic chemistry could be present in interstellar matter.

?

I guess if work like this makes a significant contribution to the OOL problem then you'll just say it existed in the first place due to ID via fine tuning or some such. That's the problem with your position. One step back is always available, no matter what.

Neal, Yockey's work made it abundantly clear that there are nothing in the physicochemical world that can account for the origin of information in the origin of life.

How do you account for the origin of information in the origin of life?

Intelligent design?

So do I calculate the FSCI in that by counting the letters that make up I-N-T-E-L-L-I-G-E-N-T D-E-S-I-G-N? Or what? Or do you have a more detailed answer? As you certainly give the impression that you do have an answer.

But I guess that's just bluffing. Or is it? Will you let slip this secret ID revelation?

In chapter 11 his arguments are being brought together to assess the origin of information in the first life. In 11.2.1 he explains his view of "unknowable":

"Thus, quantum transitions are unknowable to us but they are not impossible. They occur exponentially in time and that proves their appearance is random. Some people may believe that quantum mechanics is too esoteric to have any relation to ordinary science and to our affairs. On the contrary, the laser that records items we purchase at the supermarket is a totally quantum mechanical device. Einstein found its operation in the mathematics of quantum mechanics. There was a long wait before its discovery in the laboratory. There is no path by reasoning from classical spectroscopy to quantum mechanics and the laser. Yockey 2005 (Information theory, evolution, and the origin of life)

This is what we all know as indeterminism.

In 11.2.2 he conclude:

"The origin of the genetic code is unknowable. I have no doubt that if the historic process leading to the origin of life were knowable it would be a process of physics and chemistry.Thus, the process of the origin of life is possible but unknowable." Yockey 2005 (Information theory, evolution, and the origin of life)

In section 11.2.3 he concludes:"As one attempts to follow the tree to its Darwinian Threshold by vertically derived sequences one encounters the effects of horizontal gene transfer as the principal driving force in early cellular evolution (Woese, 2002). This means that the earliest branches of the tree or net are not knowable." Yockey 2005 (Information theory, evolution, and the origin of life)

Neal,Because we have detected a chemical used in the production of ink floating in a distance nebula, the complete works of Shakespeare will soon be arriving via the next comet.Yes Neal, that's right. I mean, chemical evolution is absurd when compared to your origin story.

"Are you saying that blind, undirected chemical processes designed and built those [PCR] machines? "

Standard ID creationist reply. Even if scientists will successfully simulate plausible prebiotic conditions that generate self-replicating molecules (SRM's), IDCers will simply dismiss it with the "argument" that scientists intelligently designed the experiment.

All you've shown is what any reasonable person would probably accept, and I certainly do. The exact sequence of events leading to the origin of life will probably never be known.

This means that the earliest branches of the tree or net are not knowable.

Yes, indeed. And this is a problem because....?

It's a problem for you because you crave exact answers. You crave an authority to tell you what do to, what to think, how to behave, what the origin of life was (poof!).

The enterprise known as science is content to know that the exact origin of life will probably never be known. Some plausible scenarios will be developed. Computer simulations will advance in power over the coming decades. Eventually it'll just be another gap for you to retreat from and move into the next one - the origin of the chemicals that enabled life to start, or the fine tuning of the laws that allowed it.

Hah.

Wake me up when you have some answers, rather then gloating at what you perceive as a weakness in science. It's not. Would you prefer OOL not be investigated because there was no chance of a definitive answer? I guess you would.

Yockey's work made it abundantly clear that there are nothing in the physicochemical world that can account for the origin of information in the origin of life.

No, it does not. Better go quotemine another bit because what you posted does not make that claim at all. It says it's probably not possible to reconstruct exactly what happened but not that nature cannot account for it!

There is a significant difference and it's dishonest of you to pretend otherwise. No wonder he has a "I'm not a creationist" note on his website, because of people like you.

With some of Yockey's insight shared, I would love to see Darwinists fall over their incompetence to comprehend the implication of indeterministic origins of life.

P.S. Everybody belief that the origin of life is possible as Yockey mentioned, that is the only sane thing to conclude from observing life all around us. The crux remains deterministic vs. indeterministic.

"The origin of the genetic code is unknowable. I have no doubt that if the historic process leading to the origin of life were knowable it would be a process of physics and chemistry.Thus, the process of the origin of life is possible but unknowable." Yockey 2005 (Information theory, evolution, and the origin of life)"

Unknowable, in the historical sense that we will never know exactly how life on earth originated 3.5 billion years ago. But not unknowable in the sense that we cannot know a number of plausible scenarios. The best evidence that I can think of would be to observe the process in real time at some far away planet. That's not gonna happen for a long while.

So now it is official, the real science stopper is Quantum Mechanics'(QM) indeterminism intruding on life science. Because the materialists decreed that "thou shalt never know this and thou shalt never study the origin of QM"